D3: Diversity, Difficulty, and Dependability-Aware Data Selection for Sample-Efficient LLM Instruction Tuning

Recent advancements in instruction tuning for large language models (LLMs) suggest that a small, high-quality dataset can significantly equip LLMs with instruction-following capabilities, outperforming large datasets often burdened by quality and redundancy issues. However, the challenge lies in automatically identifying valuable subsets from large datasets to boost both the effectiveness and efficiency of instruction tuning. In this paper, we first establish data selection criteria based on three distinct aspects of data value: diversity, difficulty, and dependability, and then propose the D3 method comprising two key steps of scoring and selection. Specifically, in the scoring step, we define the diversity function to measure sample distinctiveness and introduce the uncertainty-based prediction difficulty to evaluate sample difficulty by mitigating the interference of context-oriented generation diversity. Additionally, we integrate an external LLM for dependability assessment. In the selection step, we formulate the D3 weighted coreset objective, which jointly optimizes three aspects of data value to solve for the most valuable subset. The two steps of D3 can iterate multiple rounds, incorporating feedback to refine the selection focus adaptively. Experiments on three datasets demonstrate the effectiveness of D3 in endowing LLMs with competitive or even superior instruction-following capabilities using less than 10% of the entire dataset.

X-GAN: A Generative AI-Powered Unsupervised Model for High-Precision Segmentation of Retinal Main Vessels toward Early Detection of Glaucoma

Structural changes in main retinal blood vessels serve as critical biomarkers for the onset and progression of glaucoma. Identifying these vessels is vital for vascular modeling yet highly challenging. This paper proposes X-GAN, a generative AI-powered unsupervised segmentation model designed for extracting main blood vessels from Optical Coherence Tomography Angiography (OCTA) images. The process begins with the Space Colonization Algorithm (SCA) to rapidly generate a skeleton of vessels, featuring their radii. By synergistically integrating generative adversarial networks (GANs) with biostatistical modeling of vessel radii, X-GAN enables a fast reconstruction of both 2D and 3D representations of the vessels. Based on this reconstruction, X-GAN achieves nearly 100\% segmentation accuracy without relying on labeled data or high-performance computing resources. Also, to address the Issue, data scarity, we introduce GSS-RetVein, a high-definition mixed 2D and 3D glaucoma retinal dataset. GSS-RetVein provides a rigorous benchmark due to its exceptionally clear capillary structures, introducing controlled noise for testing model robustness. Its 2D images feature sharp capillary boundaries, while its 3D component enhances vascular reconstruction and blood flow prediction, supporting glaucoma progression simulations. Experimental results confirm GSS-RetVein's superiority in evaluating main vessel segmentation compared to existing datasets. Code and dataset are here: https://github.com/VikiXie/SatMar8.

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems

Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost-driven by high-order tensor product (TP) operations-restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network that incorporates adaptive sparsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70 percent. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact.

\underline{E2}Former: A Linear-time \underline{E}fficient and \underline{E}quivariant Trans\underline{former} for Scalable Molecular Modeling

Equivariant Graph Neural Networks (EGNNs) have demonstrated significant success in modeling microscale systems, including those in chemistry, biology and materials science. However, EGNNs face substantial computational challenges due to the high cost of constructing edge features via spherical tensor products, making them impractical for large-scale systems. To address this limitation, we introduce E2Former, an equivariant and efficient transformer architecture that incorporates the Wigner $6j$ convolution (Wigner $6j$ Conv). By shifting the computational burden from edges to nodes, the Wigner $6j$ Conv reduces the complexity from $O(|\mathcal{E}|)$ to $ O(| \mathcal{V}|)$ while preserving both the model's expressive power and rotational equivariance. We show that this approach achieves a 7x-30x speedup compared to conventional $\mathrm{SO}(3)$ convolutions. Furthermore, our empirical results demonstrate that the derived E2Former mitigates the computational challenges of existing approaches without compromising the ability to capture detailed geometric information. This development could suggest a promising direction for scalable and efficient molecular modeling.

Latent Relationship Mining of Glaucoma Biomarkers: a TRI-LSTM based Deep Learning

In recently years, a significant amount of research has been conducted on applying deep learning methods for glaucoma classification and detection. However, the explainability of those established machine learning models remains a big concern. In this research, in contrast, we learn from cognitive science concept and study how ophthalmologists judge glaucoma detection. Simulating experts' efforts, we propose a hierarchical decision making system, centered around a holistic set of carefully designed biomarker-oriented machine learning models. While biomarkers represent the key indicators of how ophthalmologists identify glaucoma, they usually exhibit latent inter-relations. We thus construct a time series model, named TRI-LSTM, capable of calculating and uncovering potential and latent relationships among various biomarkers of glaucoma. Our model is among the first efforts to explore the intrinsic connections among glaucoma biomarkers. We monitor temporal relationships in patients' disease states over time and to capture and retain the progression of disease-relevant clinical information from prior visits, thereby enriching biomarker's potential relationships. Extensive experiments over real-world dataset have demonstrated the effectiveness of the proposed model.

Temporal Graph Neural Network-Powered Paper Recommendation on Dynamic Citation Networks

Due to the rapid growth of scientific publications, identifying all related reference articles in the literature has become increasingly challenging yet highly demanding. Existing methods primarily assess candidate publications from a static perspective, focusing on the content of articles and their structural information, such as citation relationships. There is a lack of research regarding how to account for the evolving impact among papers on their embeddings. Toward this goal, this paper introduces a temporal dimension to paper recommendation strategies. The core idea is to continuously update a paper's embedding when new citation relationships appear, enhancing its relevance for future recommendations. Whenever a citation relationship is added to the literature upon the publication of a paper, the embeddings of the two related papers are updated through a Temporal Graph Neural Network (TGN). A learnable memory update module based on a Recurrent Neural Network (RNN) is utilized to study the evolution of the embedding of a paper in order to predict its reference impact in a future timestamp. Such a TGN-based model learns a pattern of how people's views of the paper may evolve, aiming to guide paper recommendations more precisely. Extensive experiments on an open citation network dataset, including 313,278 articles from https://paperswithcode.com/about PaperWithCode, have demonstrated the effectiveness of the proposed approach.

Enabling Small Models for Zero-Shot Classification through Model Label Learning

Vision-language models (VLMs) like CLIP have demonstrated impressive zero-shot ability in image classification tasks by aligning text and images but suffer inferior performance compared with task-specific expert models. On the contrary, expert models excel in their specialized domains but lack zero-shot ability for new tasks. How to obtain both the high performance of expert models and zero-shot ability is an important research direction. In this paper, we attempt to demonstrate that by constructing a model hub and aligning models with their functionalities using model labels, new tasks can be solved in a zero-shot manner by effectively selecting and reusing models in the hub. We introduce a novel paradigm, Model Label Learning (MLL), which bridges the gap between models and their functionalities through a Semantic Directed Acyclic Graph (SDAG) and leverages an algorithm, Classification Head Combination Optimization (CHCO), to select capable models for new tasks. Compared with the foundation model paradigm, it is less costly and more scalable, i.e., the zero-shot ability grows with the sizes of the model hub. Experiments on seven real-world datasets validate the effectiveness and efficiency of MLL, demonstrating that expert models can be effectively reused for zero-shot tasks. Our code will be released publicly.